Bioinformatic Teaching Resources – For Educators, by Educators – Using KBase, a Free, User-Friendly, Open Source Platform

Ellen G. Dow, Elisha M. Wood-Charlson, Steven J. Biller, Timothy Paustian, Aaron Schirmer, Cody S. Sheik, Jason M. Whitham, Rose Krebs, Carlos C. Goller, Benjamin Allen, Zachary Crockett, Adam P. Arkin

Research output: Contribution to journalArticlepeer-review

1 Scopus citations

Abstract

Over the past year, biology educators and staff at the U.S. Department of Energy Systems Biology Knowledgebase (KBase) initiated a collaborative effort to develop a curriculum for bioinformatics education. KBase is a free web-based platform where anyone can conduct sophisticated and reproducible bioinformatic analyses via a graphical user interface. Here, we demonstrate the utility of KBase as a platform for bioinformatics education, and present a set of modular, adaptable, and customizable instructional units for teaching concepts in Genomics, Metagenomics, Pangenomics, and Phylogenetics. Each module contains teaching resources, publicly available data, analysis tools, and Markdown capability, enabling instructors to modify the lesson as appropriate for their specific course. We present initial student survey data on the effectiveness of using KBase for teaching bioinformatic concepts, provide an example case study, and detail the utility of the platform from an instructor’s perspective. Even as in-person teaching returns, KBase will continue to work with instructors, supporting the development of new active learning curriculum modules. For anyone utilizing the platform, the growing KBase Educators Organization provides an educators network, accompanied by community-sourced guidelines, instructional templates, and peer support, for instructors wishing to use KBase within a classroom at any educational level–whether virtual or in-person.

Original languageEnglish (US)
Article number711535
JournalFrontiers in Education
Volume6
DOIs
StatePublished - Oct 29 2021

Bibliographical note

Funding Information:
KBase and its related work is supported as part of the Genomic Sciences Program DOE Systems Biology Knowledgebase (KBase) funded by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research under Award Numbers DE-AC02-05CH11231, DE-AC02-06CH11357, DE-AC05-00OR22725, and DE-AC02-98CH10886.

Publisher Copyright:
Copyright © 2021 Dow, Wood-Charlson, Biller, Paustian, Schirmer, Sheik, Whitham, Krebs, Goller, Allen, Crockett and Arkin.

Keywords

  • STEM education and learning
  • bioinformatics
  • computational biology
  • data science
  • undergraduate education

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